# HG changeset patch
# User Dmitriy Morozov <dmitriy@mrzv.org>
# Date 1242335083 25200
# Node ID beff535b53ff7f063d0ebb81cc8f992132edc94e
# Parent fc8ebbae62e2fa57718116ff07057ef8c8ba61b0
Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h
diff -r fc8ebbae62e2 -r beff535b53ff examples/cohomology/rips-pairwise-cohomology.cpp
--- a/examples/cohomology/rips-pairwise-cohomology.cpp Thu May 14 13:09:06 2009 -0700
+++ b/examples/cohomology/rips-pairwise-cohomology.cpp Thu May 14 14:04:43 2009 -0700
@@ -2,6 +2,7 @@
#include <topology/rips.h>
#include <geometry/l2distance.h>
+#include <geometry/distances.h>
#include <utilities/containers.h> // for BackInsertFunctor
#include <utilities/timer.h>
diff -r fc8ebbae62e2 -r beff535b53ff examples/consistency/rips-consistency-zigzag.cpp
--- a/examples/consistency/rips-consistency-zigzag.cpp Thu May 14 13:09:06 2009 -0700
+++ b/examples/consistency/rips-consistency-zigzag.cpp Thu May 14 14:04:43 2009 -0700
@@ -2,6 +2,7 @@
#include <topology/zigzag-persistence.h>
#include <geometry/l2distance.h> // Point, PointContainer, L2DistanceType, read_points
+#include <geometry/distances.h>
#include <utilities/types.h>
#include <utilities/containers.h>
diff -r fc8ebbae62e2 -r beff535b53ff examples/fitness/avida-rips-distance.cpp
--- a/examples/fitness/avida-rips-distance.cpp Thu May 14 13:09:06 2009 -0700
+++ b/examples/fitness/avida-rips-distance.cpp Thu May 14 14:04:43 2009 -0700
@@ -7,6 +7,8 @@
#include <topology/rips.h>
#include <topology/static-persistence.h>
+#include <geometry/distances.h> // for ExplicitDistances
+
typedef ExplicitDistances<AvidaPopulationDetail> ExplicitDist;
typedef Rips<ExplicitDist> RipsGen;
diff -r fc8ebbae62e2 -r beff535b53ff examples/rips/rips-image-zigzag.cpp
--- a/examples/rips/rips-image-zigzag.cpp Thu May 14 13:09:06 2009 -0700
+++ b/examples/rips/rips-image-zigzag.cpp Thu May 14 14:04:43 2009 -0700
@@ -8,6 +8,7 @@
#include <utilities/timer.h>
#include <geometry/l2distance.h> // for L2Distance and read_points()
+#include <geometry/distances.h>
#include <map>
#include <cmath>
diff -r fc8ebbae62e2 -r beff535b53ff examples/rips/rips-pairwise.cpp
--- a/examples/rips/rips-pairwise.cpp Thu May 14 13:09:06 2009 -0700
+++ b/examples/rips/rips-pairwise.cpp Thu May 14 14:04:43 2009 -0700
@@ -5,6 +5,7 @@
#include <topology/persistence-diagram.h>
#include <geometry/l2distance.h>
+#include <geometry/distances.h>
#include <utilities/containers.h> // for BackInsertFunctor
#include <utilities/timer.h>
diff -r fc8ebbae62e2 -r beff535b53ff examples/rips/rips-zigzag.cpp
--- a/examples/rips/rips-zigzag.cpp Thu May 14 13:09:06 2009 -0700
+++ b/examples/rips/rips-zigzag.cpp Thu May 14 14:04:43 2009 -0700
@@ -4,6 +4,7 @@
#include <utilities/containers.h>
#include <geometry/l2distance.h> // Point, PointContainer, L2DistanceType, read_points
+#include <geometry/distances.h>
#include <utilities/log.h>
#include <utilities/memory.h> // for report_memory()
diff -r fc8ebbae62e2 -r beff535b53ff include/geometry/distances.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/include/geometry/distances.h Thu May 14 14:04:43 2009 -0700
@@ -0,0 +1,69 @@
+#ifndef __DISTANCES_H__
+#define __DISTANCES_H__
+
+/**
+ * Class: ExplicitDistances
+ * Stores the pairwise distances of Distances_ instance passed at construction.
+ * It's a protypical Distances template argument for the Rips complex.
+ */
+template<class Distances_>
+class ExplicitDistances
+{
+ public:
+ typedef Distances_ Distances;
+ typedef size_t IndexType;
+ typedef typename Distances::DistanceType DistanceType;
+
+ ExplicitDistances(IndexType size):
+ size_(size),
+ distances_(size*(size + 1)/2 + size) {}
+ ExplicitDistances(const Distances& distances);
+
+ DistanceType operator()(IndexType a, IndexType b) const;
+ DistanceType& operator()(IndexType a, IndexType b);
+
+ size_t size() const { return size_; }
+ IndexType begin() const { return 0; }
+ IndexType end() const { return size(); }
+
+ private:
+ std::vector<DistanceType> distances_;
+ size_t size_;
+};
+
+
+/**
+ * Class: PairwiseDistances
+ * Given a Container_ of points and a Distance_, it computes distances between elements
+ * in the container (given as instances of Index_ defaulted to unsigned) using the Distance_ functor.
+ *
+ * Container_ is assumed to be an std::vector. That simplifies a number of things.
+ */
+template<class Container_, class Distance_, typename Index_ = unsigned>
+class PairwiseDistances
+{
+ public:
+ typedef Container_ Container;
+ typedef Distance_ Distance;
+ typedef Index_ IndexType;
+ typedef typename Distance::result_type DistanceType;
+
+
+ PairwiseDistances(const Container& container,
+ const Distance& distance = Distance()):
+ container_(container), distance_(distance) {}
+
+ DistanceType operator()(IndexType a, IndexType b) const { return distance_(container_[a], container_[b]); }
+
+ size_t size() const { return container_.size(); }
+ IndexType begin() const { return 0; }
+ IndexType end() const { return size(); }
+
+ private:
+ const Container& container_;
+ Distance distance_;
+};
+
+#include "distances.hpp"
+
+#endif // __DISTANCES_H__
diff -r fc8ebbae62e2 -r beff535b53ff include/geometry/distances.hpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/include/geometry/distances.hpp Thu May 14 14:04:43 2009 -0700
@@ -0,0 +1,30 @@
+template<class Distances_>
+ExplicitDistances<Distances_>::
+ExplicitDistances(const Distances& distances):
+ size_(distances.size()), distances_((distances.size() * (distances.size() + 1))/2)
+{
+ IndexType i = 0;
+ for (typename Distances::IndexType a = distances.begin(); a != distances.end(); ++a)
+ for (typename Distances::IndexType b = a; b != distances.end(); ++b)
+ {
+ distances_[i++] = distances(a,b);
+ }
+}
+
+template<class Distances_>
+typename ExplicitDistances<Distances_>::DistanceType
+ExplicitDistances<Distances_>::
+operator()(IndexType a, IndexType b) const
+{
+ if (a > b) std::swap(a,b);
+ return distances_[a*size_ - ((a*(a-1))/2) + (b-a)];
+}
+
+template<class Distances_>
+typename ExplicitDistances<Distances_>::DistanceType&
+ExplicitDistances<Distances_>::
+operator()(IndexType a, IndexType b)
+{
+ if (a > b) std::swap(a,b);
+ return distances_[a*size_ - ((a*(a-1))/2) + (b-a)];
+}
diff -r fc8ebbae62e2 -r beff535b53ff include/topology/rips.h
--- a/include/topology/rips.h Thu May 14 13:09:06 2009 -0700
+++ b/include/topology/rips.h Thu May 14 14:04:43 2009 -0700
@@ -171,65 +171,6 @@
};
-/**
- * Class: ExplicitDistances
- * Stores the pairwise distances of Distances_ instance passed at construction.
- * It's a protypical Distances template argument for the Rips complex.
- */
-template<class Distances_>
-class ExplicitDistances
-{
- public:
- typedef Distances_ Distances;
- typedef size_t IndexType;
- typedef typename Distances::DistanceType DistanceType;
-
- ExplicitDistances(const Distances& distances);
-
- DistanceType operator()(IndexType a, IndexType b) const;
-
- size_t size() const { return size_; }
- IndexType begin() const { return 0; }
- IndexType end() const { return size(); }
-
- private:
- std::vector<DistanceType> distances_;
- size_t size_;
-};
-
-
-/**
- * Class: PairwiseDistances
- * Given a Container_ of points and a Distance_, it computes distances between elements
- * in the container (given as instances of Index_ defaulted to unsigned) using the Distance_ functor.
- *
- * Container_ is assumed to be an std::vector. That simplifies a number of things.
- */
-template<class Container_, class Distance_, typename Index_ = unsigned>
-class PairwiseDistances
-{
- public:
- typedef Container_ Container;
- typedef Distance_ Distance;
- typedef Index_ IndexType;
- typedef typename Distance::result_type DistanceType;
-
-
- PairwiseDistances(const Container& container,
- const Distance& distance = Distance()):
- container_(container), distance_(distance) {}
-
- DistanceType operator()(IndexType a, IndexType b) const { return distance_(container_[a], container_[b]); }
-
- size_t size() const { return container_.size(); }
- IndexType begin() const { return 0; }
- IndexType end() const { return size(); }
-
- private:
- const Container& container_;
- Distance distance_;
-};
-
#include "rips.hpp"
#endif // __RIPS_H__
diff -r fc8ebbae62e2 -r beff535b53ff include/topology/rips.hpp
--- a/include/topology/rips.hpp Thu May 14 13:09:06 2009 -0700
+++ b/include/topology/rips.hpp Thu May 14 14:04:43 2009 -0700
@@ -195,25 +195,3 @@
mx = std::max(mx, distances_(*a,*b));
return mx;
}
-
-template<class Distances_>
-ExplicitDistances<Distances_>::
-ExplicitDistances(const Distances& distances):
- size_(distances.size()), distances_((distances.size() * (distances.size() + 1))/2)
-{
- IndexType i = 0;
- for (typename Distances::IndexType a = distances.begin(); a != distances.end(); ++a)
- for (typename Distances::IndexType b = a; b != distances.end(); ++b)
- {
- distances_[i++] = distances(a,b);
- }
-}
-
-template<class Distances_>
-typename ExplicitDistances<Distances_>::DistanceType
-ExplicitDistances<Distances_>::
-operator()(IndexType a, IndexType b) const
-{
- if (a > b) std::swap(a,b);
- return distances_[a*size_ - ((a*(a-1))/2) + (b-a)];
-}